Detailed view for PF3D7_1125300

Basic information

TDR Targets ID: 1733
Plasmodium falciparum, DNA-directed RNA polymerase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.6161 | Length (AA): 1531 | MW (Da): 179990 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00940   DNA-dependent RNA polymerase
PF14700   DNA-directed RNA polymerase N-terminal

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0005739   mitochondrion  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  
GO:0006350   transcription  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 17 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
675 1531 1msw (D) 2 883 22.00 0 1 0.52 -0.17
854 1531 1msw (D) 218 883 26.00 0 1 0.42 -0.53
48 228 4uos (A) 2 184 13.00 0.029 0.05 0.276323 -1.09
112 261 3mcm (A) 179 374 27.00 0.94 0.95 0.279875 0.37
125 372 3n3m (A) 4 238 18.00 0.0038 0.67 0.280786 0.35
146 317 4u5a (C) 47 239 18.00 0.035 0.04 0.262145 -0.39
157 396 4xmr (A) 40 261 25.00 0.62 0.75 0.15766 0.68
393 562 4uos (A) 2 183 22.00 0.27 0.96 0.373839 -0.7
634 1531 1msw (D) 2 883 22.00 0 1 0.674645 0.36
658 1531 4boc (A) 385 1230 25.00 0 1 0.737969 -0.13
868 1531 4boc (A) 594 1230 32.00 0 1 0.638603 0.29
18 106 3q8t (A) 175 263 8.00 0.22 0 0.0960149 -0.11
68 174 4ll8 (E) 64 175 19.00 0.66 0.01 0.220691 -0.46
73 620 3nc1 (A) 504 1049 9.00 0 1 -0.0648959 0.9
393 562 4uos (A) 2 183 22.00 0.062 1 0.377607 -0.72
550 1503 4boc (A) 321 1230 23.00 0 1 0.722531 0.58
840 1503 4boc (A) 594 1230 32.00 0 1 0.646783 0.29

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Sporozoite. Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Oocyst, Female Gametocyte. Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, late trophozoite, Ring, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_127975)

Species Accession Gene Product
Arabidopsis thaliana AT5G15700   DNA-directed RNA polymerase 2
Arabidopsis thaliana AT1G68990   DNA-directed RNA polymerase 1, mitochondrial
Arabidopsis thaliana AT2G24120   DNA-directed RNA polymerase 3
Babesia bovis BBOV_III002990   DNA-dependent RNA polymerase, putative
Brugia malayi Bm1_24475   DNA-dependent RNA polymerase family protein
Candida albicans CaO19.13462   Mitochondrial RNA polymerase
Candida albicans CaO19.6041   Mitochondrial RNA polymerase
Caenorhabditis elegans CELE_Y105E8A.23   Protein Y105E8A.23, isoform A
Dictyostelium discoideum DDB_G0267416   DNA-dependent RNA polymerase
Drosophila melanogaster Dmel_CG4644   mitochondrial RNA polymerase
Echinococcus granulosus EgrG_000150100   t3:t7 bacteriophage mitochodrial
Echinococcus multilocularis EmuJ_000150100   t3:t7 bacteriophage mitochodrial
Homo sapiens ENSG00000099821   polymerase (RNA) mitochondrial (DNA directed)
Leishmania braziliensis LbrM.24.1170   mitochondrial DNA-directed RNA polymerase, putative
Leishmania donovani LdBPK_241180.1   DNA-directed RNA polymerase, mitochondrial
Leishmania infantum LinJ.24.1180   mitochondrial DNA-directed RNA polymerase, putative
Leishmania major LmjF.24.1150   mitochondrial DNA-directed RNA polymerase, putative
Leishmania mexicana LmxM.24.1150   mitochondrial DNA-directed RNA polymerase, putative
Loa Loa (eye worm) LOAG_10422   DNA-dependent RNA polymerase
Mus musculus ENSMUSG00000020329   polymerase (RNA) mitochondrial (DNA directed)
Neospora caninum NCLIV_063080   DNA-directed RNA polymerase (EC 2.7.7.6), related
Oryza sativa 4346491   Os09g0246200
Oryza sativa 4341695   Os06g0652000
Plasmodium berghei PBANKA_0923000   DNA-directed RNA polymerase, putative
Plasmodium falciparum PF3D7_1125300   DNA-directed RNA polymerase
Plasmodium knowlesi PKNH_0923200   DNA-directed RNA polymerase, putative
Plasmodium vivax PVX_091885   DNA-dependent RNA polymerase, putative
Plasmodium yoelii PY06560   DNA-dependent RNA polymerase-related
Plasmodium yoelii PY06559   DNA-dependent RNA polymerase-related
Saccharomyces cerevisiae YFL036W   Rpo41p
Schistosoma japonicum Sjp_0010530   ko:K00960 DNA-directed RNA polymerase [EC2.7.7.6], putative
Schistosoma mansoni Smp_148720   t3/t7 bacteriophage-related mitochodrial DNA-directed rna polymerase
Schmidtea mediterranea mk4.000959.08  
Schmidtea mediterranea mk4.000959.09   DNA-directed RNA polymerase, mitochondrial
Trypanosoma brucei gambiense Tbg972.11.6520   mitochondrial DNA-directed RNA polymerase, putative
Trypanosoma brucei Tb927.11.5780   DNA-directed RNA polymerase, mitochondrial
Trypanosoma congolense TcIL3000.11.6160   DNA-directed RNA polymerase, mitochondrial
Trypanosoma congolense TcIL3000_0_56560   mitochondrial DNA-directed RNA polymerase
Trypanosoma cruzi TcCLB.508641.260   DNA-directed RNA polymerase, mitochondrial
Toxoplasma gondii TGME49_246060   DNA-dependent RNA polymerase
Theileria parva TP01_0975   DNA-directed RNA polymerase, putative

Essentiality

PF3D7_1125300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.3530 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.3530 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.3530 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.3530 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y105E8A.23 Caenorhabditis elegans slow growth wormbase
TGME49_246060 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

  • Assay for Ribonucleic Acid Polymerase (2.7.7.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

16 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier PF3D7_1125300 (Plasmodium falciparum), DNA-directed RNA polymerase
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